[BioC] Summarize with RMA using Alternative CDF

[Laurent Gautier]

Sean Davis wrote:
> On Fri, Jan 23, 2009 at 8:32 AM, Arteaga Salas, Jose M
> <jmarte at essex.ac.uk>wrote:
> 
>> Dear List,
>>
>> I am running an experiment with some HG-U133A arrays.
>> I identified some dodgy probes, and I have created an alternative CDF
>> file without these probes.
>>
>> Now, I want to summarize my .CEL files with either rma() or just.rma()
>> to analyze the impact of my dodgy probes in gene expression.
>>
>>
>> I am trying to run these commands, and then obtaining this error:
>>
>>> data=ReadAffy(cdfname="MyAlternativeCdf.CDF");
>>> rma.alternative=rma(data,cdfname=" MyAlternativeCdf.CDF ");
>> Error in getCdfInfo(object) :
>>  Could not obtain CDF environment, problems encountered:
>> Specified environment does not contain MyAlternativeCdf.CDF
>> Library - package MyAlternativeCdf.cdf not installed
>> Bioconductor - MyAlternativeCdf.cdf not available
>>
>>
>> My guess so far is that I am getting this error because of the C
>> implementation of RMA, that I don't seem to have available in any folder
>> of my "affy" package instalation.
>>
>>
>> Is there anyway that I can get around this problem?
>>
> 
> Actually, the problem is that you need to build a cdf environment.  The cdf
> file is not directly useful for bioconductor.  The package makecdfenv will
> do this for you.  Just work through the vignette.

You can also check the package altcdfenvs if you consider working on 
alternative CDF environmnents without wanting to handle CDF files.



L.


> Hope that helps.
> 
> Sean
> 
> 	[[alternative HTML version deleted]]
> 
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